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Omar NA, Kumar J, Teoh SL. Parkinson's disease model in zebrafish using intraperitoneal MPTP injection. Front Neurosci 2023; 17:1236049. [PMID: 37694115 PMCID: PMC10485380 DOI: 10.3389/fnins.2023.1236049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Introduction Parkinson's disease (PD) is the second most common neurodegenerative disease that severely affects the quality of life of patients and their family members. Exposure to 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) has been shown to reflect behavioral, molecular, and proteomic features of PD. This study aimed to assess the protocol for inducing PD following MPTP injection in adult zebrafish. Methods Fish were injected with 100 μg/g of MPTP intraperitoneally once or twice and then assessed on days 1 to 30 post-injection. Results Between one-time and two-time injections, there was no significant difference in most locomotor parameters, expressions of tyrosine hydroxylase-2 (th2) and dopamine transporter (dat) genes, and dopaminergic neurons (tyrosine hydroxylase positive, TH+ cells) counts. However, caspase-3 levels significantly differed between one- and two-time injections on the day 1 assessment. Discussion Over a 30-day period, the parameters showed significant differences in swimming speed, total distance traveled, tyrosine hydroxylase-1 (th1) and dat gene expressions, caspase-3 and glutathione protein levels, and TH+ cell counts. Days 3 and 5 showed the most changes compared to the control. In conclusion, a one-time injection of MPTP with delayed assessment on days 3 to 5 is a good PD model for animal studies.
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Affiliation(s)
- Noor Azzizah Omar
- Department of Anatomy, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
- Department of Medical Sciences, Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Bandar Baru Nilai, Malaysia
| | - Jaya Kumar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Seong Lin Teoh
- Department of Anatomy, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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2
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Palomino J, Gómez C, Otarola MT, Dettleff P, Patiño-García D, Orellana R, Moreno RD. Embryo Buoyancy and Cell Death Gene Expression During Embryogenesis of Yellow-Tail Kingfish Seriola lalandi. Front Cell Dev Biol 2021; 9:630947. [PMID: 33816479 PMCID: PMC8012911 DOI: 10.3389/fcell.2021.630947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/09/2021] [Indexed: 11/13/2022] Open
Abstract
In pelagic fish, embryo buoyancy is a noteworthy aspect of the reproductive strategy, and is associated with overall quality, survival, and further developmental success. In captivity, the loss of buoyancy of early embryos correlates with high mortality that might be related to massive cell death. Therefore, the aim of this study was to evaluate under captivity conditions the expression of genes related to the apoptosis process during the early embryonic development of the pelagic fish Seriola lalandi, and its relationship to the buoyancy of embryos. The relative expression of bcl2, bax-like, casp9, casp8, and casp3 was evaluated by RT-qPCR and FasL/Fas protein levels by western blot in five development stages of embryos sorted as floating or low-floating. All genes examined were expressed in both floating and low-floating embryos up to 24 h of development. Expression of the pro-apoptotic factors bax, casp9, casp8, and casp3 was higher in low-floating as compared with floating embryos in a developmental stage-specific manner. In contrast, there was no difference in expression of bcl2 between floating and low-floating embryos. Fas protein was detected as a single band in floating embryos without changes in expression throughout development; however, in low-floating embryos, three higher intensity reactive bands were detected in the 24-h embryos. Interestingly, FasL was only detected at 24-h in floating embryos, whereas in low-floating samples this ligand was present at all stages, with a sharp increase as development progressed. Cell death, as evaluated by the terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling assay, was highly increased in low-floating embryos as compared to floating embryos throughout all developmental stages, with the highest levels observed during the gastrula stage and at 24 h. The results of this study suggest that an increase in cell death, probably associated with the intrinsic and extrinsic apoptosis pathways, is present in low-floating embryos that might explain their lower developmental potential under captivity conditions.
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Affiliation(s)
- Jaime Palomino
- Departamento de Ciencias Fisiológicas, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Laboratorio de Reproducción Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Camila Gómez
- Laboratorio de Reproducción Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - María Teresa Otarola
- Departamento de Ciencias Fisiológicas, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Laboratorio de Reproducción Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Phillip Dettleff
- Laboratorio FAVET-INBIOGEN, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile.,Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Sede La Florida, Santiago, Chile
| | - Daniel Patiño-García
- Departamento de Ciencias Fisiológicas, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Ciencias Quiímicas y Biológicas, Facultad de Salud, Universidad Bernardo O'Higgins, Santiago, Chile
| | - Renan Orellana
- Departamento de Ciencias Fisiológicas, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Ciencias Quiímicas y Biológicas, Facultad de Salud, Universidad Bernardo O'Higgins, Santiago, Chile
| | - Ricardo D Moreno
- Departamento de Ciencias Fisiológicas, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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3
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Tixeira R, Poon IKH. Disassembly of dying cells in diverse organisms. Cell Mol Life Sci 2019; 76:245-257. [PMID: 30317529 PMCID: PMC11105331 DOI: 10.1007/s00018-018-2932-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 01/09/2023]
Abstract
Programmed cell death (PCD) is a conserved phenomenon in multicellular organisms required to maintain homeostasis. Among the regulated cell death pathways, apoptosis is a well-described form of PCD in mammalian cells. One of the characteristic features of apoptosis is the change in cellular morphology, often leading to the fragmentation of the cell into smaller membrane-bound vesicles through a process called apoptotic cell disassembly. Interestingly, some of these morphological changes and cell disassembly are also noted in cells of other organisms including plants, fungi and protists while undergoing 'apoptosis-like PCD'. This review will describe morphologic features leading to apoptotic cell disassembly, as well as its regulation and function in mammalian cells. The occurrence of cell disassembly during cell death in other organisms namely zebrafish, fly and worm, as well as in other eukaryotic cells will also be discussed.
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Affiliation(s)
- Rochelle Tixeira
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Ivan K H Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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Miccoli A, Dalla Valle L, Carnevali O. The maternal control in the embryonic development of zebrafish. Gen Comp Endocrinol 2017; 245:55-68. [PMID: 27013380 DOI: 10.1016/j.ygcen.2016.03.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/16/2016] [Accepted: 03/19/2016] [Indexed: 12/13/2022]
Abstract
The maternal control directing the very first hours of life is of pivotal importance for ensuring proper development to the growing embryo. Thanks to the finely regulated inheritance of maternal factors including mRNAs and proteins produced during oogenesis and stored into the mature oocyte, the embryo is sustained throughout the so-called maternal-to-zygotic transition, a period in development characterized by a species-specific length in time, during which critical biological changes regarding cell cycle and zygotic transcriptional activation occur. In order not to provoke any kind of persistent damage, the process must be delicately balanced. Surprisingly, our knowledge as to the possible effects of beneficial bacteria regarding the modulation of the quality and/or quantity of both maternally-supplied and zygotically-transcribed mRNAs, is very limited. To date, only one group has investigated the consequences of the parentally-supplied Lactobacillus rhamnosus on the storage of mRNAs into mature oocytes, leading to an altered maternal control process in the F1 generation. Particular attention was called on the monitoring of several biomarkers involved in autophagy, apoptosis and axis patterning, while data on miRNA generation and pluripotency maintenance are herein presented for the first time, and can assist in laying the ground for further investigations in this field. In this review, the reader is supplied with the current knowledge on the above-mentioned biological process, first by drawing the general background and then by emphasizing the most important findings that have highlighted their focal role in normal animal development.
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Affiliation(s)
- Andrea Miccoli
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | | | - Oliana Carnevali
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.
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5
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AnvariFar H, Amirkolaie AK, Miandare HK, Ouraji H, Jalali MA, Üçüncü Sİ. Apoptosis in fish: environmental factors and programmed cell death. Cell Tissue Res 2016; 368:425-439. [PMID: 28035476 DOI: 10.1007/s00441-016-2548-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/18/2016] [Indexed: 10/20/2022]
Abstract
Apoptosis, a form of programmed cell death, is a critical component in maintaining homeostasis and growth in all tissues and plays a significant role in immunity and cytotoxicity. In contrast to necrosis or traumatic cell death, apoptosis is a well-controlled and vital process characterized mainly by cytoplasmic shrinkage, chromatin condensation, DNA fragmentation, membrane blebbing and apoptotic bodies. Our understanding of apoptosis is partly based on observations in invertebrates but mainly in mammals. Despite the great advantages of fish models in studying vertebrate development and diseases and the tremendous interest observed in recent years, reports on apoptosis in fish are still limited. Although apoptotic machinery is well conserved between aquatic and terrestrial organisms throughout the history of evolution, some differences exist in key components of apoptotic pathways. Core parts of apoptotic machinery in fish are virtually expressed as equivalent to the mammalian models. Some differences are, however, evident, such as the extrinsic and intrinsic pathways of apoptosis including lack of a C-terminal region in the Fas-associated protein with a death domain in fish. Aquatic species inhabit a complex and highly fluctuating environment, making these species good examples to reveal features of apoptosis that may not be easily investigated in mammals. Therefore, in order to gain a wider view on programmed cell death in fish, interactions between the main environmental factors, chemicals and apoptosis are discussed in this review. It is indicated that apoptosis can be induced in fish by exposure to environmental stressors during different stages of the fish life cycle.
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Affiliation(s)
- Hossein AnvariFar
- Faculty of Animal Science and Fisheries, Department of Fisheries, University of Agriculture and Natural Resources, P.O. Box 578, Sari, Iran. .,University of Applied Science and Technology, Provincial Unit, P.O. Box: 4916694338, Golestan, Iran.
| | - Abdolsamad Keramat Amirkolaie
- Faculty of Animal Science and Fisheries, Department of Fisheries, University of Agriculture and Natural Resources, P.O. Box 578, Sari, Iran
| | - Hamed Kolangi Miandare
- Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, 49138-15739, Iran
| | - Hossein Ouraji
- Faculty of Animal Science and Fisheries, Department of Fisheries, University of Agriculture and Natural Resources, P.O. Box 578, Sari, Iran
| | - M Ali Jalali
- Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, 49138-15739, Iran.,Sturgeon Affairs Management, Gorgan, Golestan, Iran.,Center for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Victoria, 3280, Australia
| | - Sema İşisağ Üçüncü
- Faculty of Science, Department of Biology, Ege University, Bornova, 35100, İzmir, Turkey
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6
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Tucker MB, MacKenzie SH, Maciag JJ, Dirscherl Ackerman H, Swartz P, Yoder JA, Hamilton PT, Clay Clark A. Phage display and structural studies reveal plasticity in substrate specificity of caspase-3a from zebrafish. Protein Sci 2016; 25:2076-2088. [PMID: 27577093 PMCID: PMC5079243 DOI: 10.1002/pro.3032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 08/02/2016] [Accepted: 08/25/2016] [Indexed: 01/27/2023]
Abstract
The regulation of caspase-3 enzyme activity is a vital process in cell fate decisions leading to cell differentiation and tissue development or to apoptosis. The zebrafish, Danio rerio, has become an increasingly popular animal model to study several human diseases because of their transparent embryos, short reproductive cycles, and ease of drug administration. While apoptosis is an evolutionarily conserved process in metazoans, little is known about caspases from zebrafish, particularly regarding substrate specificity and allosteric regulation compared to the human caspases. We cloned zebrafish caspase-3a (casp3a) and examined substrate specificity of the recombinant protein, Casp3a, compared to human caspase-3 (CASP3) by utilizing M13 bacteriophage substrate libraries that incorporated either random amino acids at P5-P1' or aspartate fixed at P1. The results show a preference for the tetrapeptide sequence DNLD for both enzymes, but the P4 position of zebrafish Casp3a also accommodates valine equally well. We determined the structure of zebrafish Casp3a to 2.28Å resolution by X-ray crystallography, and when combined with molecular dynamics simulations, the results suggest that a limited number of amino acid substitutions near the active site result in plasticity of the S4 sub-site by increasing flexibility of one active site loop and by affecting hydrogen-bonding with substrate. The data show that zebrafish Casp3a exhibits a broader substrate portfolio, suggesting overlap with the functions of caspase-6 in zebrafish development.
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Affiliation(s)
- Matthew B Tucker
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, North Carolina, 27608
| | - Sarah H MacKenzie
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, North Carolina, 27608
| | - Joseph J Maciag
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, North Carolina, 27608
| | | | - Paul Swartz
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, North Carolina, 27608
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, North Carolina, 27608
| | - Paul T Hamilton
- Department of Plant and Microbial Biology, NC State University, Raleigh, North Carolina, 27608
| | - A Clay Clark
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019.
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7
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Barreiro-Iglesias A, Mysiak KS, Scott AL, Reimer MM, Yang Y, Becker CG, Becker T. Serotonin Promotes Development and Regeneration of Spinal Motor Neurons in Zebrafish. Cell Rep 2015; 13:924-32. [PMID: 26565906 PMCID: PMC4635313 DOI: 10.1016/j.celrep.2015.09.050] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/13/2015] [Accepted: 09/17/2015] [Indexed: 12/26/2022] Open
Abstract
In contrast to mammals, zebrafish regenerate spinal motor neurons. During regeneration, developmental signals are re-deployed. Here, we show that, during development, diffuse serotonin promotes spinal motor neuron generation from pMN progenitor cells, leaving interneuron numbers unchanged. Pharmacological manipulations and receptor knockdown indicate that serotonin acts at least in part via 5-HT1A receptors. In adults, serotonin is supplied to the spinal cord mainly (90%) by descending axons from the brain. After a spinal lesion, serotonergic axons degenerate caudal to the lesion but sprout rostral to it. Toxin-mediated ablation of serotonergic axons also rostral to the lesion impaired regeneration of motor neurons only there. Conversely, intraperitoneal serotonin injections doubled numbers of new motor neurons and proliferating pMN-like progenitors caudal to the lesion. Regeneration of spinal-intrinsic serotonergic interneurons was unaltered by these manipulations. Hence, serotonin selectively promotes the development and adult regeneration of motor neurons in zebrafish.
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Affiliation(s)
- Antón Barreiro-Iglesias
- Centre for Neuroregeneration, Edinburgh Medical School, Biomedical Sciences, The Chancellor's Building, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Karolina S Mysiak
- Centre for Neuroregeneration, Edinburgh Medical School, Biomedical Sciences, The Chancellor's Building, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Angela L Scott
- Centre for Neuroregeneration, Edinburgh Medical School, Biomedical Sciences, The Chancellor's Building, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Michell M Reimer
- Centre for Neuroregeneration, Edinburgh Medical School, Biomedical Sciences, The Chancellor's Building, University of Edinburgh, Edinburgh EH16 4SB, UK; Technische Universität Dresden, DFG-Center for Regenerative Therapies Dresden, Cluster of Excellence at the TU Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Yujie Yang
- Centre for Neuroregeneration, Edinburgh Medical School, Biomedical Sciences, The Chancellor's Building, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Catherina G Becker
- Centre for Neuroregeneration, Edinburgh Medical School, Biomedical Sciences, The Chancellor's Building, University of Edinburgh, Edinburgh EH16 4SB, UK; Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh EH16 4SB, UK.
| | - Thomas Becker
- Centre for Neuroregeneration, Edinburgh Medical School, Biomedical Sciences, The Chancellor's Building, University of Edinburgh, Edinburgh EH16 4SB, UK; Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh EH16 4SB, UK.
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8
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Diotel N, Vaillant C, Gabbero C, Mironov S, Fostier A, Gueguen MM, Anglade I, Kah O, Pellegrini E. Effects of estradiol in adult neurogenesis and brain repair in zebrafish. Horm Behav 2013; 63:193-207. [PMID: 22521210 DOI: 10.1016/j.yhbeh.2012.04.003] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 04/03/2012] [Accepted: 04/04/2012] [Indexed: 12/21/2022]
Abstract
The brain of the adult teleost fish exhibits intense neurogenic activity and an outstanding capability for brain repair. Remarkably, the brain estrogen-synthesizing enzyme, aromatase B, is strongly expressed, particularly in adult fishes, in radial glial cells, which act as progenitors. Using zebrafish, we tested the hypothesis that estrogens affect adult neurogenesis and brain regeneration by modulating the neurogenic activity of radial glial cells. To investigate this, the estrogenic environment was modified through inhibition of aromatase activity, blockade of nuclear estrogen receptors, or estrogenic treatments. Estrogens significantly decreased cell proliferation and migration at the olfactory bulbs/telencephalon junction and in the mediobasal hypothalamus. It also appears that cell survival is reduced at the olfactory bulbs/telencephalon junction. We also developed a model of telencephalic lesion to assess the role of aromatase and estrogens in brain repair. Proliferation increased rapidly immediately after the lesion in the parenchyma of the injured telencephalon, while proliferation at the ventricular surface appeared after 48 h and peaked at 7 days. At this time, most proliferative cells express Sox2, however, none of these Sox2 positive cells correspond to aromatase B-positive radial glial cells. Interestingly, aromatase B expression was significantly reduced 48 h and 7 days after the injury, but surprisingly, at 72 h after lesion, aromatase B expression appeared de novo expressed in parenchyma cells, suggesting a role for this ectopic expression of aromatase in brain repair mechanisms. Altogether these data suggest that estrogens modulate adult, but not reparative neurogenesis, in zebrafish.
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Affiliation(s)
- Nicolas Diotel
- Neuroendocrine Effects of Endocrine Disruptors, Inserm, IRSET, U1085, Université de Rennes 1, Rennes, France
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9
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Valencia CA, Zou J, Liu R. In vitro selection of proteins with desired characteristics using mRNA-display. Methods 2012. [PMID: 23201412 DOI: 10.1016/j.ymeth.2012.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
mRNA-display is an amplification-based, iterative rounds of in vitro protein selection technique that circumvents a number of difficulties associated with yeast two-hybrid and phage display. Because of the covalent linkage between the genotype and the phenotype, mRNA-display provides a powerful means for reading and amplifying a peptide or protein sequence after it has been selected from a library with very high diversity. The purpose of this article is to provide a summary of the field and practical framework of mRNA-display-based selections. We summarize the advantages and limitations of selections using mRNA-display as well as the recent applications, namely, the identification of novel affinity reagents, target-binding partners, and enzyme substrates from synthetic peptide or natural proteome libraries. Practically, we provide a detailed procedure for performing mRNA-display-based selections with the aim of identifying protease substrates and binding partners of a target protein. Furthermore, we describe how to confirm the function of the selected protein sequences by biochemical assays and bioinformatic tools.
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Affiliation(s)
- C Alexander Valencia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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Abstract
The caspases are unique proteases that mediate the major morphological changes of apoptosis and various other cellular remodeling processes. As we catalog and study the myriad proteins subject to cleavage by caspases, we are beginning to appreciate the full functional repertoire of these enzymes. Here, we examine current knowledge about caspase cleavages: what kinds of proteins are cut, in what contexts, and to what end. After reviewing basic caspase biology, we describe the technologies that enable high-throughput caspase substrate discovery and the datasets they have yielded. We discuss how caspases recognize their substrates and how cleavages are conserved among different metazoan organisms. Rather than comprehensively reviewing all known substrates, we use examples to highlight some functional impacts of caspase cuts during apoptosis and differentiation. Finally, we discuss the roles caspase substrates can play in medicine. Though great progress has been made in this field, many important areas still await exploration.
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Affiliation(s)
- Emily D Crawford
- Department of Pharmaceutical Chemistry and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158-2330, USA.
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Generation and characterization of antibodies specific for caspase-cleaved neo-epitopes: a novel approach. Cell Death Dis 2011; 2:e205. [PMID: 21881607 PMCID: PMC3186909 DOI: 10.1038/cddis.2011.91] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Apoptosis research has been significantly aided by the generation of antibodies against caspase-cleaved peptide neo-epitopes. However, most of these antibodies recognize the N-terminal fragment and are specific for the protein in question. The aim of this project was to create antibodies, which could identify caspase-cleaved proteins without a priori knowledge of the cleavage sites or even the proteins themselves. We hypothesized that many caspase-cleavage products might have a common antigenic shape, given that they must all fit into the same active site of caspases. Rabbits were immunized with the eight most prevalent exposed C-terminal tetrapeptide sequences following caspase cleavage. After purification of the antibodies we demonstrated (1) their specificity for exposed C-terminal (but not internal) peptides, (2) their ability to detect known caspase-cleaved proteins from apoptotic cell lysates or supernatants from apoptotic cell culture and (3) their ability to detect a caspase-cleaved protein whose tetrapeptide sequence differs from the eight tetrapeptides used to generate the antibodies. These antibodies have the potential to identify novel neo-epitopes produced by caspase cleavage and so can be used to identify pathway-specific caspase cleavage events in a specific cell type. Additionally this methodology may be applied to generate antibodies against products of other proteases, which have a well-defined and non-promiscuous cleavage activity.
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Loynes CA, Martin JS, Robertson A, Trushell DMI, Ingham PW, Whyte MKB, Renshaw SA. Pivotal Advance: Pharmacological manipulation of inflammation resolution during spontaneously resolving tissue neutrophilia in the zebrafish. J Leukoc Biol 2010; 87:203-12. [PMID: 19850882 PMCID: PMC2812557 DOI: 10.1189/jlb.0409255] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Zebrafish are a unique model for pharmacological manipulation of physiological processes such as inflammation; they are small and permeable to many small molecular compounds, and being transparent, they permit the visualization and quantitation of the inflammatory response by observation of transgenically labeled inflammatory cell populations. Using a transgenic line specifically labeling neutrophils in vivo (mpx:GFP), we studied the effects of a range of pharmacological agents on the resolution of inflammation in vivo. These agents were selected for their ability to modulate neutrophil function and lifespan in human neutrophils in vitro. Agents delaying neutrophil apoptosis (LPS, dbcAMP, and several caspase inhibitors) all lead to a delay in resolution of neutrophilic inflammation. Reciprocally, pyocyanin and roscovitine (inducers of neutrophil apoptosis) lead to reduced neutrophil numbers. The occurrence of apoptosis was observed by time-lapse analysis and confirmed by dual staining for neutrophil-specific mpx activity (TSA staining) and an apoptotic marker (TUNEL). During inflammation, macrophages follow neutrophils into the inflamed site, and TUNEL/TSA dual-positive material can be demonstrated within macrophages, consistent with their uptake of apoptotic neutrophils. This model has several advantages over mammalian models and lends itself to the study of pharmaceutical agents modulating inflammation.
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Affiliation(s)
- Catherine A Loynes
- MRC Centre for Developmental and Biomedical Genetics, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
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14
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Demon D, Van Damme P, Vanden Berghe T, Vandekerckhove J, Declercq W, Gevaert K, Vandenabeele P. Caspase substrates: easily caught in deep waters? Trends Biotechnol 2009; 27:680-8. [PMID: 19879007 DOI: 10.1016/j.tibtech.2009.09.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 09/18/2009] [Accepted: 09/22/2009] [Indexed: 11/29/2022]
Abstract
Caspases are key players in various cellular processes, such as apoptosis, proliferation and differentiation, and in pathological conditions including cancer and inflammation. Although caspases preferentially cleave C-terminal of aspartic acid residues, their action is restricted generally to one or a few sites per protein substrate. Caspase-specific substrate recognition appears to be determined by the substrate sequences adjacent to the scissile bond. Knowledge of these substrates and the generated fragments is crucial for a thorough understanding of the functional implications of caspase-mediated proteolysis. In addition, insight into the cleavage specificity might assist in designing inhibitors that target disease-related caspase activities. Here, we critically review recently published procedures used to generate a proteome-wide view of caspase substrates.
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Affiliation(s)
- Dieter Demon
- Department for Molecular Biomedical Research, VIB, B-9052 Ghent, Belgium
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15
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Krumschnabel G, Podrabsky JE. Fish as model systems for the study of vertebrate apoptosis. Apoptosis 2008; 14:1-21. [PMID: 19082731 DOI: 10.1007/s10495-008-0281-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 11/17/2008] [Indexed: 01/18/2023]
Abstract
Apoptosis is a process of pivotal importance for multi-cellular organisms and due to its implication in the development of cancer and degenerative disease it is intensively studied in humans and mammalian model systems. Invertebrate models of apoptosis have been well-studied, especially in C. elegans and D. melanogaster, but as these are evolutionarily distant from mammals the relevance of findings for human research is sometimes limited. Presently, a non-mammalian vertebrate model for studying apoptosis is missing. However, in the past few years an increasing number of studies on cell death in fish have been published and thus new model systems may emerge. This review aims at highlighting the most important of these findings, showing similarities and dissimilarities between fish and mammals, and will suggest topics for future research. In addition, the outstanding usefulness of fish as research models will be pointed out, hoping to spark future research on this exciting, often underrated group of vertebrates.
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Affiliation(s)
- Gerhard Krumschnabel
- Division of Developmental Immunology, Biocenter, Innsbruck Medical University, 6020 Innsbruck, Austria.
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Van Damme P, Vandekerckhove J, Gevaert K. Disentanglement of protease substrate repertoires. Biol Chem 2008; 389:371-81. [PMID: 18208357 DOI: 10.1515/bc.2008.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Identification of protease substrates and detailed characterization of processed sites are essential for understanding the biological function of proteases. Because of inherent complexity reasons, this however remains a formidable analytical challenge, illustrated by the fact that the majority of the more than 500 human proteases are uncharacterized to date. Recently, in addition to conventional genetic and biochemical approaches, diverse quantitative peptide-centric proteomics approaches, some of which selectively recover N-terminal peptides, have emerged. These latter proteomic technologies in particular allow the identification of natural protease substrates and delineation of cleavage sites in a complex, natural background of thousands of different proteins. We here review current biochemical, genetic and proteomic methods for global analysis of substrates of proteases and discuss selected applications.
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Affiliation(s)
- Petra Van Damme
- Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology (VIB), B-9000 Ghent, Belgium
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Chowdhury I, Tharakan B, Bhat GK. Caspases - an update. Comp Biochem Physiol B Biochem Mol Biol 2008; 151:10-27. [PMID: 18602321 DOI: 10.1016/j.cbpb.2008.05.010] [Citation(s) in RCA: 259] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 05/23/2008] [Accepted: 05/23/2008] [Indexed: 02/07/2023]
Abstract
Caspases belong to a family of highly conserved aspartate-specific cysteine proteases and are members of the interleukin-1beta-converting enzyme family, present in multicellular organisms. The caspase gene family consists of 15 mammalian members that are grouped into two major sub-families, namely inflammatory caspases and apoptotic caspases. The apoptotic caspases are further subdivided into two sub-groups, initiator caspases and executioner caspases. The caspases form a caspase-cascade system that plays the central role in the induction, transduction and amplification of intracellular apoptotic signals for cell fate determination, regulation of immunity, and cellular proliferation and differentiation. The substrates of apoptotic caspases have been associated with cellular dismantling, while inflammatory caspases mediate the proteolytic activation of inflammatory cytokines. The activation of this delicate caspase-cascade system and its functions are regulated by a variety of regulatory molecules, such as the inhibitor of apoptosis protein (IAP), FLICE, calpain, and Ca(2+). Based on the available literature we have reviewed and discussed the members of the caspase family, caspase-cascade system, caspase-regulating molecules and their apoptotic and non-apoptotic functions in cellular life and death. Also recent progress in the molecular structure and physiological role of non-mammalian caspases such as paracaspases, metacaspases and caspase-like-protease family members are included in relation to that of mammalian species.
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Affiliation(s)
- Indrajit Chowdhury
- Department of Obstetrics and Gynecology, Morehouse School of Medicine, 720 Westview Drive, SW., Atlanta, GA 30310, USA
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Modulation of nucleobindin-1 and nucleobindin-2 by caspases. FEBS Lett 2007; 582:286-90. [PMID: 18154733 DOI: 10.1016/j.febslet.2007.12.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 11/30/2007] [Accepted: 12/08/2007] [Indexed: 11/22/2022]
Abstract
Nucleobindin-1 (NUCB1) and nucleobindin-2 (NUCB2) are multifunctional proteins that interact with Ca(2+), nucleic acids and various regulatory proteins in different signaling pathways. So far, our understanding of the regulation of the biological functions of nucleobindins remains limited. In our proteome-wide selection for downstream caspase substrates, both NUCB1 and NUCB2 are found to be the downstream substrates of caspases. We report here the detailed analyses of the cleavage of nucleobindins by caspases. Significantly, the caspase cleavage sites are located exactly at one of the Ca(2+)-binding EF-hand motifs. Our results suggest that the functions of nucleobindins could be modulated by caspase-mediated cleavage in apoptosis.
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Valencia CA, Cotten SW, Liu R. Cleavage of BNIP-2 and BNIP-XL by caspases. Biochem Biophys Res Commun 2007; 364:495-501. [PMID: 17961507 DOI: 10.1016/j.bbrc.2007.10.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 10/06/2007] [Indexed: 11/30/2022]
Abstract
BNIP-2 and BNIP-XL are BCH domain-containing proteins that are implicated in programmed cell death. It has been reported that overexpression of BNIP-2 in neuroblastoma cell lines resulted in massive cell death, whereas BNIP-XL was upregulated during NGF-depletion-induced apoptosis in neuroblastoma and was involved in the regulation of differentiation, survival, and aggressiveness of tumor cells. Despite their importance in apoptosis, our understanding of BNIP-2 containing proteins is limited. In this communication, we demonstrate that both BNIP-2 and BNIP-XL are cleaved by caspases during apoptosis. Significantly, the caspase cleavage sites on BNIP-2 are located on its N-terminal EF-hand motif, while that on BNIP-XL is located upstream of the C-terminal BCH domain. Our results suggest that the caspase-mediated cleavage of BNIP-2 and BNIP-XL could result in the release of the BCH domain or smaller fragments that are crucial for their proapoptotic activities.
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Affiliation(s)
- C Alexander Valencia
- School of Pharmacy and Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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